[Bioc-devel] BioC 2.5: Added scanDates slot to Biobase's eSet class

Laurent,
The scan dates were singled out originally because we have  
encountered data sets at the Hutch that appear to have a scan date  
effect and wanted a location to store this information so it can be  
included in the analysis. As you mentioned, there are other  
variables that could be important as well and shouldn't be ignored.

Given that you have been actively working towards a solution of  
managing array metadata, you can help create a design that can be  
implemented in the Biobase package. Martin Morgan is currently  
leading this effort and we can start a dialog off-list (so as not to  
spam the rest of the developers with minutiae) with those who are  
interested to hammer out a solution to this problem. I think once  
the requirements are formally expressed, we can easily put together  
a design that meets the user's needs.


Patrick



Laurent Gautier wrote:

Patrick,

The conceptual distinction you want to make can be seen as  
artificial.

When you start introducing "arrayData" as a separated entity, you  
will soon have to introduce "samplepreparationData" (what  
extraction protocol was used, where there any biopsy, etc...),  
"imageAnalysisData" (you know grid alignment, spot segmentation).  
Is it reasonable to add a slot each time ? Moreover, those  
categories can probably also be broken down into subcategories.  
Finally, what is making the scanning date so important ?
Wouldn't the version of the software used, or the scanner, or the  
scanner settings, or the name of the person who performed the  
scanning be of relevance ?

One route would be to construct an initial AnnotatedDataFrame and  
populate it with whatever you fancy from the raw-data files (scan  
date, software, etc...). I have been going way with my homebrew  
infrastructure, and it has so far been leading to quite much  
expressivity. Reserved words are not necessarily very limiting (if  
sufficiently specific, say "array_scan_date" and the associated  
varMetaData = "Date when scanning the hybridized microarray"), and  
I'd think better to carefully design and document what is happening  
when one is trying to add an other column with the same name rather  
than rely on security-through-obscurity with mangled names.



L.





Patrick Aboyoun wrote:

Laurent,
As you mentioned the existing phenoData infrastructure could be  
used to house information like scan dates, scanner model, and  
scanning software version, but this information is not  
conceptually phenotype data and, and adding it to an  
AnnotatedDataFrame comes with the limitation of using reserved  
words (maybe name mangled like .__ScanDates__?) for column names  
in the AnnotatedDataFrame.

The internal discussion we have been having to making this more  
general is to add a different slot (candidate name arrayData) to  
eSet (and removing the scanDates slot) that would house the type  
of information we have been discussing in a combination of  
dedicated slots like scanDates and a catch all AnnotatedDataFrame  
slot for less universal data. This design would separate the array  
data from the phenotype data and having dedicating slots for  
important information like scan dates would avoid having to manage  
special columns in an AnnotatedDataFrame.

As you rightly point out we need to ensure we support a rich suite  
of functionality like "[", subset, etc., but this can all be  
handled through methods for the eSet class.

Keep in mind that this recent change is just a first step, not a  
final design, and with your help and input from the rest of the  
BioC developer community, we can ensure we end up with a  
sufficiently useful microarray data infrastructure.

Cheers,
Patrick


Quoting Laurent Gautier <laurent at cbs.dtu.dk>:

Patrick,

There are indeed always several ways to address needs, and my  
comment
is mostly pointing at the fact that creating yet-an-other slot is  
not
necessary since one can currently store such data into phenoData  
(into
a column named... say "scan_date").

I would in fact qualify of overbuilding the approach that adds a  
new
(and exclusive) slot while improving the exiting infrastructure  
could
perfectly answer the needs. So today it's "scanDates", and next  
could
be "scannerModel", or "scanningSoftwareVersion".

I have been a little unclear (even to myself) in my comment about  
using
"[", so here are more details. *If* the extract operator was made  
to
evaluate expressions such as the function subset() does, or in  
fact if
a method subset was implemented for eSet objects, storing all
information into phenoData makes such things nice:

# silly example: only get the control data scanned in the future:
eset[, scan_date > date() & treatment == "control"]
# same with subset:
subset(eset, , scan_date > date() & treatment == "control")

# a little longer to write
eset[, scanDates(eset) > date() & pData(eset) == "control"]


If for some reasons a distinction between phenoData and
like-phenoData-but-can't-be-the-same is needed, please do  
consider the
creation of an AnnotatedDataFrame that contains all of them.



L.





Patrick Aboyoun wrote:

Laurent,
We had some immediate need for scan date information and rather   
than overbuild a system for managing metadata that we may or  
may  not need, we opted to start simply and then build up as   
appropriate. There has been some internal discussions about   
managing other metadata along with scan dates, but nothing else  
has  bubbled to the top yet. Your thoughts and design can help  
speed up  this process. The class versioning system in Biobase  
supports  iterative development and we can make further changes  
once we lock  a design in place. One editorial comment I have is  
that lots of  designs are possible for a given need and, for  
example, the current  class properly subsets the scanDates  
information using "[" despite  not being stored in the phenoData  
(AnnotatedDataFrame) slot.


Cheers,
Patrick


Quoting Laurent Gautier <laurent at cbs.dtu.dk>:

Hi Patrick,

Storing the scan dates is indeed useful information, and is it  
nice to
have it offered at the parsing stage.
However, first comment would be "does it justify a new slot" to  
eSet ?

I have been storing scan dates for quite some time now, but  
opted for
having them in the phenoData as it made more sense to me, both  
on an
implementation standpoint and on practical standpoint (as  
standard
extraction of an eset-subset on columns with the "[" operator  
works).

If having something specific for scan dates is really really  
wished,
would it make make sense to have that by extending  
AnnotatedDataFrame ?

In my opinion, the stage at which the the data are extracted  
(in that
case when parsing the files coming out of the image analysis)  
should
not dictate where the data are stored.
In fact, it might make it for a nice(r) workflow if the function
reading raw array data could return an eSet-inheriting instance  
and a
phenoData with information such as dates and file names. I am  
working
on a workflow that is in fact getting much more data from the  
header (I
suppose that I'd contribute it when enough time to wrap it up).


Just few thoughts,



L.





Patrick Aboyoun wrote:

Dear Bioconductor developers,
The Biocore group has just committed a change to the BioC 2.5   
code  line (Biobase version 2.5.3) to support the use of   
microarray scan  date in statistical analyses by adding a   
scanDates slot to  Biobase's eSet class. This information can  
be  retrieved and set  using the new scanDates and  
scanDates<-  function respectively. The  scanDates slot is  
designed to hold a  character vector of length = #  of  
samples, with one character  element for each sample. (See   
help(scanDates) for more  information.)

In this first round of check-ins we have added affy support  
of  this  new slot to functions like ReadAffy and we will be  
working  towards  adding this information to other microarray  
platforms as  well.

This change involved bumping the eSet version number from  
1.1.0  to  1.2.0 in the Biobase class definition. In order to  
minimize  the  impact of this change, the Biobase methods  
support both the  current  eSet version 1.2.0 as well as old  
1.1.0 serialized  objects so  updateObject will not be  
required to be performed on  eSet-derived  objects prior to  
use in other functions. We have  also tested and  versioned  
bumped (and patched where needed) the  following packages   
that create eSet-derived classes to minimize  any package  
build  issues: ACME, beadarray, beadarraySNP,  cellHTS2,  
CGHbase, codelink,  crlmm, GeneRegionScan, GGBase,  maDB,  
oligoClasses, ontoTools, puma,  rMAT, SNPchip, and spkTools.

Below is a demonstration of the new functionality. If you   
encounter  any issues related to this change, please e-mail  
this  list so the  community can monitor the change.

- The Biocore Team

suppressMessages(library(affy))
example(ReadAffy)

RdAffy> if(require(affydata)){
RdAffy+      celpath <- system.file("celfiles",  
package="affydata")
RdAffy+      fns <- list.celfiles(path=celpath,full.names=TRUE)
RdAffy+  RdAffy+      cat("Reading  files: 
\n",paste(fns,collapse="\n"),"\n")
RdAffy+      ##read a binary celfile
RdAffy+      abatch <- ReadAffy(filenames=fns[1])
RdAffy+      ##read a text celfile
RdAffy+      abatch <- ReadAffy(filenames=fns[2])
RdAffy+      ##read all files in that dir
RdAffy+      abatch <- ReadAffy(celfile.path=celpath)
RdAffy+ }
Loading required package: affydata
Reading files:
/Library/Frameworks/R.framework/Versions/2.10/Resources/ 
library/affydata/celfiles/binary.cel   /Library/Frameworks/ 
R.framework/Versions/2.10/Resources/library/affydata/celfiles/ 
text.cel

scanDates(abatch)

     binary.cel            text.cel
"01/23/04 14:30:57" "08/29/03 15:12:30"

sessionInfo()

R version 2.10.0 Under development (unstable) (2009-06-12  
r48755)
i386-apple-darwin9.6.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets   
methods   base
other attached packages:
[1] affydata_1.11.6 affy_1.23.2     Biobase_2.5.3
loaded via a namespace (and not attached):
[1] affyio_1.13.3        preprocessCore_1.7.4 tools_2.10.0